From 91cfbb06a318cff3750d49e837fc804dc111186f Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:15:20 +0100 Subject: [PATCH 01/80] Create Dagg_2023.md --- docs/Dagg_2023.md | 1 + 1 file changed, 1 insertion(+) create mode 100644 docs/Dagg_2023.md diff --git a/docs/Dagg_2023.md b/docs/Dagg_2023.md new file mode 100644 index 00000000..935d41cd --- /dev/null +++ b/docs/Dagg_2023.md @@ -0,0 +1 @@ +## Dissecting the functional organization of the C. elegans serotonergic system at whole-brain scale From 3d7c99669f5209750179e9dc523673547f51613f Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:15:34 +0100 Subject: [PATCH 02/80] Update index.md --- docs/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/index.md b/docs/index.md index 2ab2c5c9..95e433a1 100644 --- a/docs/index.md +++ b/docs/index.md @@ -8,7 +8,7 @@ Information on published connectomics data related to _C. elegans_. This is bein | Papers | Features | Datasets | Readers | | ------------- | ----- | ----- | ---- | -| [Albertson & Thompson 1976](Albertson_Thompson_1976.md) | Anatomical | N/A | N/A | +| [Albertson & Thomson 1976](Albertson_Thompson_1976.md) | Anatomical | N/A | N/A | | [White et al. 1986](White_1986.md) | Anatomical |[N2U.txt](https://github.com/dwitvliet/nature2021/blob/0646af9d25896ae660f97d462eab2d67282f5625/data/legacy_data/wormwiring_N2U.txt)| N/A | | [Durbin 1987](Durbin_1987.md) | Anatomical |[Durbin.txt](https://github.com/dwitvliet/nature2021/blob/0646af9d25896ae660f97d462eab2d67282f5625/data/legacy_data/durbin.txt)| N/A | | [Hall & Russell 1991](Hall_1991.md) | Anatomical | N/A | N/A | From cc91c5f00c271b2766a2395953a7fd7dd6912e29 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:16:30 +0100 Subject: [PATCH 03/80] Update index.md --- docs/index.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/index.md b/docs/index.md index 95e433a1..63e94e72 100644 --- a/docs/index.md +++ b/docs/index.md @@ -8,7 +8,7 @@ Information on published connectomics data related to _C. elegans_. This is bein | Papers | Features | Datasets | Readers | | ------------- | ----- | ----- | ---- | -| [Albertson & Thomson 1976](Albertson_Thompson_1976.md) | Anatomical | N/A | N/A | +| [Albertson & Thomson 1976](Albertson_1976.md) | Anatomical | N/A | N/A | | [White et al. 1986](White_1986.md) | Anatomical |[N2U.txt](https://github.com/dwitvliet/nature2021/blob/0646af9d25896ae660f97d462eab2d67282f5625/data/legacy_data/wormwiring_N2U.txt)| N/A | | [Durbin 1987](Durbin_1987.md) | Anatomical |[Durbin.txt](https://github.com/dwitvliet/nature2021/blob/0646af9d25896ae660f97d462eab2d67282f5625/data/legacy_data/durbin.txt)| N/A | | [Hall & Russell 1991](Hall_1991.md) | Anatomical | N/A | N/A | @@ -24,6 +24,7 @@ Information on published connectomics data related to _C. elegans_. This is bein | [Taylor et al. 2021](Taylor_2021.md) | Gene Expression | [data](https://github.com/cengenproject/CeNGEN_integrated_analysis_biorxiv_code) | N/A | | [Yemini et al. 2021](Yemini_2021.md) | Gene Expression | [data](https://zenodo.org/records/3906530) | N/A | | [Beets et al. 2023](Beets_2023.md) | Gene Expression | [data](https://github.com/cengenproject/CeNGEN_integrated_analysis_biorxiv_code) | N/A | +| [Dagg et al. 2023](Dagg_2023.md) | Extrasynaptic | N/A | N/A | | [Atanas et al. 2023](Atanas_2023.md) | Functional | [data](https://www.wormwideweb.org/dataset.html) | N/A | | [Randi et al. 2023](Randi_2023.md) | Functional | [data]() | N/A | From c10feb6b6ef9f9b8804b122e004e4ca8458fc2f7 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:17:42 +0100 Subject: [PATCH 04/80] Update Dagg_2023.md --- docs/Dagg_2023.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docs/Dagg_2023.md b/docs/Dagg_2023.md index 935d41cd..a3707ff8 100644 --- a/docs/Dagg_2023.md +++ b/docs/Dagg_2023.md @@ -1 +1,9 @@ ## Dissecting the functional organization of the C. elegans serotonergic system at whole-brain scale +_Ugur Dag, Ijeoma Nwabudike, Di Kang, Matthew A. Gomes, Jungsoo Kim, Adam A. Atanas, Eric Bueno, Cassi Estrem, Sarah Pugliese, Ziyu Wang, Emma Towlson, Steven W. Flavell, +Dissecting the functional organization of the C. elegans serotonergic system at whole-brain scale, +Cell, +Volume 186, Issue 12, +2023, +Pages 2574-2592.e20, +ISSN 0092-8674, +https://doi.org/10.1016/j.cell.2023.04.023._ From c1a5d058188f6cd2d6f07a91308307431c252849 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:18:09 +0100 Subject: [PATCH 05/80] Update Dagg_2023.md --- docs/Dagg_2023.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/Dagg_2023.md b/docs/Dagg_2023.md index a3707ff8..f389eff8 100644 --- a/docs/Dagg_2023.md +++ b/docs/Dagg_2023.md @@ -1,7 +1,8 @@ ## Dissecting the functional organization of the C. elegans serotonergic system at whole-brain scale _Ugur Dag, Ijeoma Nwabudike, Di Kang, Matthew A. Gomes, Jungsoo Kim, Adam A. Atanas, Eric Bueno, Cassi Estrem, Sarah Pugliese, Ziyu Wang, Emma Towlson, Steven W. Flavell, -Dissecting the functional organization of the C. elegans serotonergic system at whole-brain scale, -Cell, +Dissecting the functional organization of the C. elegans serotonergic system at whole-brain scale_ + +_Cell, Volume 186, Issue 12, 2023, Pages 2574-2592.e20, From 1ff27cc6d3e3713af89d99af13ed575821bfaeab Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:18:22 +0100 Subject: [PATCH 06/80] Rename Dagg_2023.md to Dag_2023.md --- docs/{Dagg_2023.md => Dag_2023.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/{Dagg_2023.md => Dag_2023.md} (100%) diff --git a/docs/Dagg_2023.md b/docs/Dag_2023.md similarity index 100% rename from docs/Dagg_2023.md rename to docs/Dag_2023.md From d20a9644b7b2c79318c04137d7a5ee95d3abfeeb Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:18:51 +0100 Subject: [PATCH 07/80] Update index.md --- docs/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/index.md b/docs/index.md index 63e94e72..68503d57 100644 --- a/docs/index.md +++ b/docs/index.md @@ -24,7 +24,7 @@ Information on published connectomics data related to _C. elegans_. This is bein | [Taylor et al. 2021](Taylor_2021.md) | Gene Expression | [data](https://github.com/cengenproject/CeNGEN_integrated_analysis_biorxiv_code) | N/A | | [Yemini et al. 2021](Yemini_2021.md) | Gene Expression | [data](https://zenodo.org/records/3906530) | N/A | | [Beets et al. 2023](Beets_2023.md) | Gene Expression | [data](https://github.com/cengenproject/CeNGEN_integrated_analysis_biorxiv_code) | N/A | -| [Dagg et al. 2023](Dagg_2023.md) | Extrasynaptic | N/A | N/A | +| [Dag et al. 2023](Dag_2023.md) | Extrasynaptic | N/A | N/A | | [Atanas et al. 2023](Atanas_2023.md) | Functional | [data](https://www.wormwideweb.org/dataset.html) | N/A | | [Randi et al. 2023](Randi_2023.md) | Functional | [data]() | N/A | From e63bd8cad19e46d4cefa35290115fa4df4f2c170 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:28:05 +0100 Subject: [PATCH 08/80] Update index.md --- docs/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/index.md b/docs/index.md index 68503d57..ff7004cb 100644 --- a/docs/index.md +++ b/docs/index.md @@ -24,7 +24,7 @@ Information on published connectomics data related to _C. elegans_. This is bein | [Taylor et al. 2021](Taylor_2021.md) | Gene Expression | [data](https://github.com/cengenproject/CeNGEN_integrated_analysis_biorxiv_code) | N/A | | [Yemini et al. 2021](Yemini_2021.md) | Gene Expression | [data](https://zenodo.org/records/3906530) | N/A | | [Beets et al. 2023](Beets_2023.md) | Gene Expression | [data](https://github.com/cengenproject/CeNGEN_integrated_analysis_biorxiv_code) | N/A | -| [Dag et al. 2023](Dag_2023.md) | Extrasynaptic | N/A | N/A | +| [Dag et al. 2023](Dag_2023.md) | Functional | N/A | N/A | | [Atanas et al. 2023](Atanas_2023.md) | Functional | [data](https://www.wormwideweb.org/dataset.html) | N/A | | [Randi et al. 2023](Randi_2023.md) | Functional | [data]() | N/A | From 6e51315cdf25e32af5ce9b553bd56fbd3613f4ca Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:30:05 +0100 Subject: [PATCH 09/80] Update Albertson_1976.md --- docs/Albertson_1976.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/Albertson_1976.md b/docs/Albertson_1976.md index ef179bd9..2f107713 100644 --- a/docs/Albertson_1976.md +++ b/docs/Albertson_1976.md @@ -1,4 +1,6 @@ ## The pharynx of Caenorhabditis elegans _Donna G. Albertson and J. N. Thompson_ +_Phil. Trans. R. Soc. Lond. B275299–325_ + _Published: 10 August 1976 https://doi.org/10.1098/rstb.1976.0085_ From 9c62606d62d8c87c2d6d3c6b20afaaed54b11afa Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:30:18 +0100 Subject: [PATCH 10/80] Update Albertson_1976.md --- docs/Albertson_1976.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/Albertson_1976.md b/docs/Albertson_1976.md index 2f107713..3235c129 100644 --- a/docs/Albertson_1976.md +++ b/docs/Albertson_1976.md @@ -1,6 +1,4 @@ ## The pharynx of Caenorhabditis elegans _Donna G. Albertson and J. N. Thompson_ - _Phil. Trans. R. Soc. Lond. B275299–325_ - _Published: 10 August 1976 https://doi.org/10.1098/rstb.1976.0085_ From 06c0bde0512521e20c251a947dfdfc94f43e5bf7 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:31:03 +0100 Subject: [PATCH 11/80] Update Albertson_1976.md --- docs/Albertson_1976.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/Albertson_1976.md b/docs/Albertson_1976.md index 3235c129..7615e1e4 100644 --- a/docs/Albertson_1976.md +++ b/docs/Albertson_1976.md @@ -1,4 +1,3 @@ ## The pharynx of Caenorhabditis elegans -_Donna G. Albertson and J. N. Thompson_ -_Phil. Trans. R. Soc. Lond. B275299–325_ +_Donna G. Albertson and J. N. Thompson_ _Phil. Trans. R. Soc. Lond. B275299–325_ _Published: 10 August 1976 https://doi.org/10.1098/rstb.1976.0085_ From 1facc9102b4f6705b880978ef927c5f9f971410b Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:31:24 +0100 Subject: [PATCH 12/80] Update Albertson_1976.md --- docs/Albertson_1976.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Albertson_1976.md b/docs/Albertson_1976.md index 7615e1e4..601aca3f 100644 --- a/docs/Albertson_1976.md +++ b/docs/Albertson_1976.md @@ -1,3 +1,3 @@ ## The pharynx of Caenorhabditis elegans -_Donna G. Albertson and J. N. Thompson_ _Phil. Trans. R. Soc. Lond. B275299–325_ +_Donna G. Albertson and J. N. Thompson_
_Phil. Trans. R. Soc. Lond. B275299–325_ _Published: 10 August 1976 https://doi.org/10.1098/rstb.1976.0085_ From 963e2a4adab5d101facb459b96a67ef41306669b Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:31:38 +0100 Subject: [PATCH 13/80] Update Albertson_1976.md --- docs/Albertson_1976.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/Albertson_1976.md b/docs/Albertson_1976.md index 601aca3f..2465f34c 100644 --- a/docs/Albertson_1976.md +++ b/docs/Albertson_1976.md @@ -1,3 +1,2 @@ ## The pharynx of Caenorhabditis elegans -_Donna G. Albertson and J. N. Thompson_
_Phil. Trans. R. Soc. Lond. B275299–325_ -_Published: 10 August 1976 https://doi.org/10.1098/rstb.1976.0085_ +_Donna G. Albertson and J. N. Thompson_
_Phil. Trans. R. Soc. Lond. B275299–325_
_Published: 10 August 1976 https://doi.org/10.1098/rstb.1976.0085_ From 2f8174f90720c1029db3cb03115900cf41b0c406 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:35:12 +0100 Subject: [PATCH 14/80] Update Albertson_1976.md --- docs/Albertson_1976.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/Albertson_1976.md b/docs/Albertson_1976.md index 2465f34c..f202eb16 100644 --- a/docs/Albertson_1976.md +++ b/docs/Albertson_1976.md @@ -1,2 +1,6 @@ ## The pharynx of Caenorhabditis elegans _Donna G. Albertson and J. N. Thompson_
_Phil. Trans. R. Soc. Lond. B275299–325_
_Published: 10 August 1976 https://doi.org/10.1098/rstb.1976.0085_ + +**Summary** +- The anatomical connectome of the pharynx has been reconstructed from serial electron micrographs. +- The connectivity of this region has been described at the level of individual synaptic regions differentiating electical gap junction connections and chemical synaptic connections. From 9a3b6715df2f240fe4b695bc007d98b4ffa38e1e Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:36:02 +0100 Subject: [PATCH 15/80] Update Albertson_1976.md --- docs/Albertson_1976.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/Albertson_1976.md b/docs/Albertson_1976.md index f202eb16..c99f766c 100644 --- a/docs/Albertson_1976.md +++ b/docs/Albertson_1976.md @@ -4,3 +4,4 @@ _Donna G. Albertson and J. N. Thompson_
_Phil. Trans. R. Soc. Lond. B27529 **Summary** - The anatomical connectome of the pharynx has been reconstructed from serial electron micrographs. - The connectivity of this region has been described at the level of individual synaptic regions differentiating electical gap junction connections and chemical synaptic connections. +- Composed of 34 muscle cells, 9 marginal cells, 9 epithelial cells, 5 gland cells and 20 neurons. From 00ae33411c18137162d3317515566af31f121441 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:39:26 +0100 Subject: [PATCH 16/80] Update Altun_2009.md --- docs/Altun_2009.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/docs/Altun_2009.md b/docs/Altun_2009.md index 231bbe19..1615e01a 100644 --- a/docs/Altun_2009.md +++ b/docs/Altun_2009.md @@ -1,6 +1,5 @@ ## High resolution map of Caenorhabditis elegans gap junction proteins -_Zeynep F.Altun, Bojun Chen, Zhao-Weng Wang, David. H Hall_ - -_Published: 17 July 2009 (https://doi.org/10.1002/dvdy.22025)_ - -There are three tables of innexin expression within the paper. Table 3 is incorporated into a [dataset](https://github.com/yasinthanvickneswaran/ConnectomeToolbox/blob/main/cect/data/Modified%20celegans%20db%20dump.csv) with WormAtlas data. +_Zeynep F.Altun, Bojun Chen, Zhao-Weng Wang, David. H Hall_
_Dev. Dyn., 238: 1936-1950_
_Published: 17 July 2009 (https://doi.org/10.1002/dvdy.22025)_ +**Summary** +- There are three tables of innexin expression within the paper. +- Table 3 is incorporated into a [dataset](https://github.com/yasinthanvickneswaran/ConnectomeToolbox/blob/main/cect/data/Modified%20celegans%20db%20dump.csv) with WormAtlas data. From 2d1e6b61a97acc832d0b6cf0e4e14baee84d84e4 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:39:36 +0100 Subject: [PATCH 17/80] Update Altun_2009.md --- docs/Altun_2009.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/Altun_2009.md b/docs/Altun_2009.md index 1615e01a..2a1f8d27 100644 --- a/docs/Altun_2009.md +++ b/docs/Altun_2009.md @@ -1,5 +1,6 @@ ## High resolution map of Caenorhabditis elegans gap junction proteins _Zeynep F.Altun, Bojun Chen, Zhao-Weng Wang, David. H Hall_
_Dev. Dyn., 238: 1936-1950_
_Published: 17 July 2009 (https://doi.org/10.1002/dvdy.22025)_ + **Summary** - There are three tables of innexin expression within the paper. - Table 3 is incorporated into a [dataset](https://github.com/yasinthanvickneswaran/ConnectomeToolbox/blob/main/cect/data/Modified%20celegans%20db%20dump.csv) with WormAtlas data. From 87abe85208c846b9a598be913c6cda51915e76fb Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:50:55 +0100 Subject: [PATCH 18/80] Update non_omv.yml --- .github/workflows/non_omv.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/non_omv.yml b/.github/workflows/non_omv.yml index bab2dc7b..820f13de 100644 --- a/.github/workflows/non_omv.yml +++ b/.github/workflows/non_omv.yml @@ -37,6 +37,7 @@ jobs: run: | pip install . pip install wormneuroatlas + pip install mkdocs-plotly-plugin pip list From 3b41ef75cdeeb08fe34562b4e785977a6a21f7bd Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:51:21 +0100 Subject: [PATCH 19/80] Update non_omv.yml --- .github/workflows/non_omv.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/non_omv.yml b/.github/workflows/non_omv.yml index 820f13de..bab2dc7b 100644 --- a/.github/workflows/non_omv.yml +++ b/.github/workflows/non_omv.yml @@ -37,7 +37,6 @@ jobs: run: | pip install . pip install wormneuroatlas - pip install mkdocs-plotly-plugin pip list From 37a742ffb9f96c985f4b5dab9f43184b06778c01 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:52:01 +0100 Subject: [PATCH 20/80] Update ci-pages.yml --- .github/workflows/ci-pages.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci-pages.yml b/.github/workflows/ci-pages.yml index 02322f8b..fc8eaa31 100644 --- a/.github/workflows/ci-pages.yml +++ b/.github/workflows/ci-pages.yml @@ -26,7 +26,10 @@ jobs: path: .cache restore-keys: | mkdocs-material- - - run: pip install mkdocs-material + - run: | + pip install mkdocs-material + pip install mkdocs-plotly-plugin + - run: mkdocs gh-deploy --force From 32572ab5c0f41b24a8d1ef129a9c820d7887d6b0 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:55:50 +0100 Subject: [PATCH 21/80] Update mkdocs.yml --- mkdocs.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/mkdocs.yml b/mkdocs.yml index 14b3585e..d16ab1be 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -6,12 +6,22 @@ theme: palette: primary: green +plugins: + - plotly + markdown_extensions: - pymdownx.superfences: custom_fences: - name: mermaid class: mermaid format: !!python/name:pymdownx.superfences.fence_code_format + - pymdownx.superfences: + custom_fences: + - name: plotly + class: plotly + format: !!python/name:mkdocs_plotly_plugin.fences.fence_plotly + + nav: - Overview: 'index.md' From f0ea1ca5f23eed9ad537329d4f5358a2060777d9 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 14:56:55 +0100 Subject: [PATCH 22/80] Update Albertson_1976.md --- docs/Albertson_1976.md | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/docs/Albertson_1976.md b/docs/Albertson_1976.md index c99f766c..8c7a3cb6 100644 --- a/docs/Albertson_1976.md +++ b/docs/Albertson_1976.md @@ -5,3 +5,24 @@ _Donna G. Albertson and J. N. Thompson_
_Phil. Trans. R. Soc. Lond. B27529 - The anatomical connectome of the pharynx has been reconstructed from serial electron micrographs. - The connectivity of this region has been described at the level of individual synaptic regions differentiating electical gap junction connections and chemical synaptic connections. - Composed of 34 muscle cells, 9 marginal cells, 9 epithelial cells, 5 gland cells and 20 neurons. + + +``` plotly +{ + "data": [ + { + "x": [ + "giraffes", + "orangutans", + "monkeys" + ], + "y": [ + 20, + 14, + 23 + ], + "type": "bar" + } + ] +} +``` From 1c1511fe7724687a34ebb8c3cab28d8adb98cd0a Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:00:10 +0100 Subject: [PATCH 23/80] Update Albertson_1976.md --- docs/Albertson_1976.md | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/docs/Albertson_1976.md b/docs/Albertson_1976.md index 8c7a3cb6..9ba710d0 100644 --- a/docs/Albertson_1976.md +++ b/docs/Albertson_1976.md @@ -6,23 +6,3 @@ _Donna G. Albertson and J. N. Thompson_
_Phil. Trans. R. Soc. Lond. B27529 - The connectivity of this region has been described at the level of individual synaptic regions differentiating electical gap junction connections and chemical synaptic connections. - Composed of 34 muscle cells, 9 marginal cells, 9 epithelial cells, 5 gland cells and 20 neurons. - -``` plotly -{ - "data": [ - { - "x": [ - "giraffes", - "orangutans", - "monkeys" - ], - "y": [ - 20, - 14, - 23 - ], - "type": "bar" - } - ] -} -``` From eb0fc7121cded0bf388ae8f539fcaf20bf062fb6 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:03:48 +0100 Subject: [PATCH 24/80] Update Albertson_1976.md --- docs/Albertson_1976.md | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/docs/Albertson_1976.md b/docs/Albertson_1976.md index 9ba710d0..6e02310b 100644 --- a/docs/Albertson_1976.md +++ b/docs/Albertson_1976.md @@ -6,3 +6,21 @@ _Donna G. Albertson and J. N. Thompson_
_Phil. Trans. R. Soc. Lond. B27529 - The connectivity of this region has been described at the level of individual synaptic regions differentiating electical gap junction connections and chemical synaptic connections. - Composed of 34 muscle cells, 9 marginal cells, 9 epithelial cells, 5 gland cells and 20 neurons. + +{ + "data": [ + { + "x": [ + "giraffes", + "orangutans", + "monkeys" + ], + "y": [ + 20, + 14, + 23 + ], + "type": "bar" + } + ] +} From f9c4ffcab99cc5a8482b17e1596586f42c75fb6d Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:05:07 +0100 Subject: [PATCH 25/80] Update Albertson_1976.md --- docs/Albertson_1976.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/Albertson_1976.md b/docs/Albertson_1976.md index 6e02310b..a2c70608 100644 --- a/docs/Albertson_1976.md +++ b/docs/Albertson_1976.md @@ -6,7 +6,7 @@ _Donna G. Albertson and J. N. Thompson_
_Phil. Trans. R. Soc. Lond. B27529 - The connectivity of this region has been described at the level of individual synaptic regions differentiating electical gap junction connections and chemical synaptic connections. - Composed of 34 muscle cells, 9 marginal cells, 9 epithelial cells, 5 gland cells and 20 neurons. - +``` plotly { "data": [ { @@ -24,3 +24,4 @@ _Donna G. Albertson and J. N. Thompson_
_Phil. Trans. R. Soc. Lond. B27529 } ] } +``` From 0045055be9f13a9ae5da6e1ff6130e5c72f901e1 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:07:50 +0100 Subject: [PATCH 26/80] Update mkdocs.yml --- mkdocs.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index d16ab1be..3e88f70f 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -15,8 +15,6 @@ markdown_extensions: - name: mermaid class: mermaid format: !!python/name:pymdownx.superfences.fence_code_format - - pymdownx.superfences: - custom_fences: - name: plotly class: plotly format: !!python/name:mkdocs_plotly_plugin.fences.fence_plotly From 2db557b9cad199e611bd7234bd79f8119be36f1a Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:08:41 +0100 Subject: [PATCH 27/80] Update Albertson_1976.md From cbf4c484037b5eeb46cd170e1eb8bdec90838f46 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:16:37 +0100 Subject: [PATCH 28/80] Update Albertson_1976.md --- docs/Albertson_1976.md | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/docs/Albertson_1976.md b/docs/Albertson_1976.md index a2c70608..c99f766c 100644 --- a/docs/Albertson_1976.md +++ b/docs/Albertson_1976.md @@ -5,23 +5,3 @@ _Donna G. Albertson and J. N. Thompson_
_Phil. Trans. R. Soc. Lond. B27529 - The anatomical connectome of the pharynx has been reconstructed from serial electron micrographs. - The connectivity of this region has been described at the level of individual synaptic regions differentiating electical gap junction connections and chemical synaptic connections. - Composed of 34 muscle cells, 9 marginal cells, 9 epithelial cells, 5 gland cells and 20 neurons. - -``` plotly -{ - "data": [ - { - "x": [ - "giraffes", - "orangutans", - "monkeys" - ], - "y": [ - 20, - 14, - 23 - ], - "type": "bar" - } - ] -} -``` From 2fec90be3eef1d2dca22fbd1b1f1a9994696936f Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:16:57 +0100 Subject: [PATCH 29/80] Update Timeline.md --- docs/Timeline.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/docs/Timeline.md b/docs/Timeline.md index 24e82eec..180d8337 100644 --- a/docs/Timeline.md +++ b/docs/Timeline.md @@ -61,7 +61,4 @@ flowchart TD K --> P NP --> P F --> P - - - ``` From 975c00a09f471db0992aa95cb44b2050ba6a2c5c Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:17:12 +0100 Subject: [PATCH 30/80] Update Timeline.md --- docs/Timeline.md | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/docs/Timeline.md b/docs/Timeline.md index 180d8337..3e4bcf6f 100644 --- a/docs/Timeline.md +++ b/docs/Timeline.md @@ -62,3 +62,23 @@ flowchart TD NP --> P F --> P ``` + +```plotly +{ + "data": [ + { + "x": [ + "giraffes", + "orangutans", + "monkeys" + ], + "y": [ + 20, + 14, + 23 + ], + "type": "bar" + } + ] +} +``` From 5cb86a7c3b2d5a66c761fa6acc1b327d4563850e Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:17:52 +0100 Subject: [PATCH 31/80] Update Timeline.md --- docs/Timeline.md | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/docs/Timeline.md b/docs/Timeline.md index 3e4bcf6f..180d8337 100644 --- a/docs/Timeline.md +++ b/docs/Timeline.md @@ -62,23 +62,3 @@ flowchart TD NP --> P F --> P ``` - -```plotly -{ - "data": [ - { - "x": [ - "giraffes", - "orangutans", - "monkeys" - ], - "y": [ - 20, - 14, - 23 - ], - "type": "bar" - } - ] -} -``` From be8472add6c37223819b225255925cf3a4783204 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:32:27 +0100 Subject: [PATCH 32/80] Update mkdocs.yml --- mkdocs.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index 3e88f70f..de91b6d4 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -22,7 +22,7 @@ markdown_extensions: nav: - - Overview: 'index.md' + - Overview: 'Timeline.md' - 'Connectomes': - 'Albertson & Thomson 1976': 'Albertson_1976.md' - 'White et al. 1986': 'White_1986.md' @@ -44,6 +44,6 @@ nav: - 'Beets et al. 2023': 'Beets_2023.md' - 'Ripoll-Sanchez et al. 2023': 'Ripoll_2023.md' - 'Randi et al. 2023': 'Randi_2023.md' - - 'Timeline': 'Timeline.md' + - 'Index': 'Timeline.md' - Python package: - 'Installation': 'Python.md' From d2a30bbb24c48b1cd9cce722841b594e54767a3a Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:35:59 +0100 Subject: [PATCH 33/80] Update mkdocs.yml --- mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index de91b6d4..749f8e07 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -44,6 +44,6 @@ nav: - 'Beets et al. 2023': 'Beets_2023.md' - 'Ripoll-Sanchez et al. 2023': 'Ripoll_2023.md' - 'Randi et al. 2023': 'Randi_2023.md' - - 'Index': 'Timeline.md' + - 'Index': 'index.md' - Python package: - 'Installation': 'Python.md' From d8fcb172e5a6837a22adb5bfe9821c17a3f7cf60 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:39:06 +0100 Subject: [PATCH 34/80] Update mkdocs.yml --- mkdocs.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/mkdocs.yml b/mkdocs.yml index 749f8e07..1d61c560 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -10,6 +10,8 @@ plugins: - plotly markdown_extensions: + - pymdownx.snippets: + base_path: ['docs'] - pymdownx.superfences: custom_fences: - name: mermaid From 85412b2ab8b0ff026b5aa94a0737671c4f8bcb0b Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:41:09 +0100 Subject: [PATCH 35/80] Create contour.json --- docs/assets/contour.json | 1 + 1 file changed, 1 insertion(+) create mode 100644 docs/assets/contour.json diff --git a/docs/assets/contour.json b/docs/assets/contour.json new file mode 100644 index 00000000..9e58223d --- /dev/null +++ b/docs/assets/contour.json @@ -0,0 +1 @@ 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From 95bfa8c2a14d143bbd7baa4dd403626616f17ac2 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:41:57 +0100 Subject: [PATCH 36/80] Update Albertson_1976.md --- docs/Albertson_1976.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/Albertson_1976.md b/docs/Albertson_1976.md index c99f766c..a8fbf6a5 100644 --- a/docs/Albertson_1976.md +++ b/docs/Albertson_1976.md @@ -5,3 +5,8 @@ _Donna G. Albertson and J. N. Thompson_
_Phil. Trans. R. Soc. Lond. B27529 - The anatomical connectome of the pharynx has been reconstructed from serial electron micrographs. - The connectivity of this region has been described at the level of individual synaptic regions differentiating electical gap junction connections and chemical synaptic connections. - Composed of 34 muscle cells, 9 marginal cells, 9 epithelial cells, 5 gland cells and 20 neurons. + + +```plotly +--8<-- "./assets/contour.json" +``` From 01ec40a249d0aedb5c03196f16f57a44f55f4d6e Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:53:44 +0100 Subject: [PATCH 37/80] Update mkdocs.yml --- mkdocs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/mkdocs.yml b/mkdocs.yml index 1d61c560..296e739c 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -13,6 +13,7 @@ markdown_extensions: - pymdownx.snippets: base_path: ['docs'] - pymdownx.superfences: + preserve_tabs: true custom_fences: - name: mermaid class: mermaid From 74702f60d063e0c6443b65357ccbdb330c01a2ab Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:07:48 +0100 Subject: [PATCH 38/80] Update Albertson_1976.md --- docs/Albertson_1976.md | 5 ----- 1 file changed, 5 deletions(-) diff --git a/docs/Albertson_1976.md b/docs/Albertson_1976.md index a8fbf6a5..c99f766c 100644 --- a/docs/Albertson_1976.md +++ b/docs/Albertson_1976.md @@ -5,8 +5,3 @@ _Donna G. Albertson and J. N. Thompson_
_Phil. Trans. R. Soc. Lond. B27529 - The anatomical connectome of the pharynx has been reconstructed from serial electron micrographs. - The connectivity of this region has been described at the level of individual synaptic regions differentiating electical gap junction connections and chemical synaptic connections. - Composed of 34 muscle cells, 9 marginal cells, 9 epithelial cells, 5 gland cells and 20 neurons. - - -```plotly ---8<-- "./assets/contour.json" -``` From 765fa7dd4a6d6ccf593e6ca8480bf83780944a66 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:08:04 +0100 Subject: [PATCH 39/80] Delete docs/assets directory --- docs/assets/contour.json | 1 - 1 file changed, 1 deletion(-) delete mode 100644 docs/assets/contour.json diff --git a/docs/assets/contour.json b/docs/assets/contour.json deleted file mode 100644 index 9e58223d..00000000 --- a/docs/assets/contour.json +++ /dev/null @@ -1 +0,0 @@ -{"data":[{"x":[-9,-6,-5,-3,-1],"y":[0,1,4,5,7],"z":[[10,10.625,12.5,15.625,20],[5.625,6.25,8.125,11.25,15.625],[2.5,3.125,5.0,8.125,12.5],[0.625,1.25,3.125,6.25,10.625],[0,0.625,2.5,5.625,10]],"type":"contour"}],"layout":{"template":{"data":{"histogram2dcontour":[{"type":"histogram2dcontour","colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0.0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1.0,"#f0f921"]]}],"choropleth":[{"type":"choropleth","colorbar":{"outlinewidth":0,"ticks":""}}],"histogram2d":[{"type":"histogram2d","colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0.0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1.0,"#f0f921"]]}],"heatmap":[{"type":"heatmap","colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0.0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1.0,"#f0f921"]]}],"heatmapgl":[{"type":"heatmapgl","colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0.0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1.0,"#f0f921"]]}],"contourcarpet":[{"type":"contourcarpet","colorbar":{"outlinewidth":0,"ticks":""}}],"contour":[{"type":"contour","colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0.0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1.0,"#f0f921"]]}],"surface":[{"type":"surface","colorbar":{"outlinewidth":0,"ticks":""},"colorscale":[[0.0,"#0d0887"],[0.1111111111111111,"#46039f"],[0.2222222222222222,"#7201a8"],[0.3333333333333333,"#9c179e"],[0.4444444444444444,"#bd3786"],[0.5555555555555556,"#d8576b"],[0.6666666666666666,"#ed7953"],[0.7777777777777778,"#fb9f3a"],[0.8888888888888888,"#fdca26"],[1.0,"#f0f921"]]}],"mesh3d":[{"type":"mesh3d","colorbar":{"outlinewidth":0,"ticks":""}}],"scatter":[{"fillpattern":{"fillmode":"overlay","size":10,"solidity":0.2},"type":"scatter"}],"parcoords":[{"type":"parcoords","line":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"scatterpolargl":[{"type":"scatterpolargl","marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"bar":[{"error_x":{"color":"#2a3f5f"},"error_y":{"color":"#2a3f5f"},"marker":{"line":{"color":"#E5ECF6","width":0.5},"pattern":{"fillmode":"overlay","size":10,"solidity":0.2}},"type":"bar"}],"scattergeo":[{"type":"scattergeo","marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"scatterpolar":[{"type":"scatterpolar","marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"histogram":[{"marker":{"pattern":{"fillmode":"overlay","size":10,"solidity":0.2}},"type":"histogram"}],"scattergl":[{"type":"scattergl","marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"scatter3d":[{"type":"scatter3d","line":{"colorbar":{"outlinewidth":0,"ticks":""}},"marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"scattermapbox":[{"type":"scattermapbox","marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"scatterternary":[{"type":"scatterternary","marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"scattercarpet":[{"type":"scattercarpet","marker":{"colorbar":{"outlinewidth":0,"ticks":""}}}],"carpet":[{"aaxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"baxis":{"endlinecolor":"#2a3f5f","gridcolor":"white","linecolor":"white","minorgridcolor":"white","startlinecolor":"#2a3f5f"},"type":"carpet"}],"table":[{"cells":{"fill":{"color":"#EBF0F8"},"line":{"color":"white"}},"header":{"fill":{"color":"#C8D4E3"},"line":{"color":"white"}},"type":"table"}],"barpolar":[{"marker":{"line":{"color":"#E5ECF6","width":0.5},"pattern":{"fillmode":"overlay","size":10,"solidity":0.2}},"type":"barpolar"}],"pie":[{"automargin":true,"type":"pie"}]},"layout":{"autotypenumbers":"strict","colorway":["#636efa","#EF553B","#00cc96","#ab63fa","#FFA15A","#19d3f3","#FF6692","#B6E880","#FF97FF","#FECB52"],"font":{"color":"#2a3f5f"},"hovermode":"closest","hoverlabel":{"align":"left"},"paper_bgcolor":"white","plot_bgcolor":"#E5ECF6","polar":{"bgcolor":"#E5ECF6","angularaxis":{"gridcolor":"white","linecolor":"white","ticks":""},"radialaxis":{"gridcolor":"white",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From f57111f03d03de8d9d7c2c70fd084d0e567b6739 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:08:51 +0100 Subject: [PATCH 40/80] Update ci-pages.yml --- .github/workflows/ci-pages.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci-pages.yml b/.github/workflows/ci-pages.yml index fc8eaa31..46ce491b 100644 --- a/.github/workflows/ci-pages.yml +++ b/.github/workflows/ci-pages.yml @@ -28,7 +28,6 @@ jobs: mkdocs-material- - run: | pip install mkdocs-material - pip install mkdocs-plotly-plugin From d0e52545a2821a905b43a8fc0c1049120376353d Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:09:31 +0100 Subject: [PATCH 41/80] Update mkdocs.yml --- mkdocs.yml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index 296e739c..c0568bd9 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -13,18 +13,13 @@ markdown_extensions: - pymdownx.snippets: base_path: ['docs'] - pymdownx.superfences: - preserve_tabs: true custom_fences: - name: mermaid class: mermaid format: !!python/name:pymdownx.superfences.fence_code_format - - name: plotly - class: plotly - format: !!python/name:mkdocs_plotly_plugin.fences.fence_plotly - -nav: + nav: - Overview: 'Timeline.md' - 'Connectomes': - 'Albertson & Thomson 1976': 'Albertson_1976.md' From f6a614e30904962e07037b7c356704b2cde37ddf Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:11:48 +0100 Subject: [PATCH 42/80] Update mkdocs.yml --- mkdocs.yml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index c0568bd9..304f942e 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -6,19 +6,13 @@ theme: palette: primary: green -plugins: - - plotly - markdown_extensions: - - pymdownx.snippets: - base_path: ['docs'] - pymdownx.superfences: custom_fences: - name: mermaid class: mermaid format: !!python/name:pymdownx.superfences.fence_code_format - nav: - Overview: 'Timeline.md' - 'Connectomes': From 79b38363768052cf02cd350c0abb8d697fa2d620 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:14:37 +0100 Subject: [PATCH 43/80] Update ci-pages.yml --- .github/workflows/ci-pages.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/ci-pages.yml b/.github/workflows/ci-pages.yml index 46ce491b..773d90e2 100644 --- a/.github/workflows/ci-pages.yml +++ b/.github/workflows/ci-pages.yml @@ -26,8 +26,7 @@ jobs: path: .cache restore-keys: | mkdocs-material- - - run: | - pip install mkdocs-material + - run: pip install mkdocs-material From 179a956c315b48140776288343f131a90c2e860d Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:16:12 +0100 Subject: [PATCH 44/80] Update mkdocs.yml --- mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index 304f942e..9fba2605 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -13,7 +13,7 @@ markdown_extensions: class: mermaid format: !!python/name:pymdownx.superfences.fence_code_format - nav: +nav: - Overview: 'Timeline.md' - 'Connectomes': - 'Albertson & Thomson 1976': 'Albertson_1976.md' From 98f86f86576b306e834f5a075ada5d765bd12e5b Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:18:39 +0100 Subject: [PATCH 45/80] Update Atanas_2023.md --- docs/Atanas_2023.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/docs/Atanas_2023.md b/docs/Atanas_2023.md index 60e31f25..1ebffa5e 100644 --- a/docs/Atanas_2023.md +++ b/docs/Atanas_2023.md @@ -1,7 +1,5 @@ ## Brain-wide representations of behavior spanning multiple timescales and states in C. elegans -_Adam A. Atanas, Jungsoo Kim, Ziyu Wang, Eric Bueno, McCoy Becker, Di Kang, Jungyeon Park, Talya S. Kramer, Flossie K. Wan, Saba Baskoylu, Ugur Dag, Elpiniki Kalogeropoulou, Matthew A. Gomes, Cassi Estrem, Netta Cohen, Vikash K. Mansinghka, and Steven W. Flavell_ - -_Published: September 14, 2023 https://doi.org/10.1016/j.cell.2023.07.035_ +_Adam A. Atanas, Jungsoo Kim, Ziyu Wang, Eric Bueno, McCoy Becker, Di Kang, Jungyeon Park, Talya S. Kramer, Flossie K. Wan, Saba Baskoylu, Ugur Dag, Elpiniki Kalogeropoulou, Matthew A. Gomes, Cassi Estrem, Netta Cohen, Vikash K. Mansinghka, and Steven W. Flavell_
_Cell, Volume 186, Issue 19, 2023, Pages 4134-4151.e31, ISSN 0092-8674_
_Published: September 14, 2023 https://doi.org/10.1016/j.cell.2023.07.035_ - For quantitative analaysis, the two adult datasets from Witvliet et al were averaged. (https://www.nature.com/articles/s41586-021-03778-8) - Self looping and single synapse edges were excluded From ef2b4b71e09b2a01ab175f3f55a0bfad5407dd3e Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:18:55 +0100 Subject: [PATCH 46/80] Update Atanas_2023.md --- docs/Atanas_2023.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/Atanas_2023.md b/docs/Atanas_2023.md index 1ebffa5e..9a7f38b9 100644 --- a/docs/Atanas_2023.md +++ b/docs/Atanas_2023.md @@ -1,5 +1,7 @@ ## Brain-wide representations of behavior spanning multiple timescales and states in C. elegans -_Adam A. Atanas, Jungsoo Kim, Ziyu Wang, Eric Bueno, McCoy Becker, Di Kang, Jungyeon Park, Talya S. Kramer, Flossie K. Wan, Saba Baskoylu, Ugur Dag, Elpiniki Kalogeropoulou, Matthew A. Gomes, Cassi Estrem, Netta Cohen, Vikash K. Mansinghka, and Steven W. Flavell_
_Cell, Volume 186, Issue 19, 2023, Pages 4134-4151.e31, ISSN 0092-8674_
_Published: September 14, 2023 https://doi.org/10.1016/j.cell.2023.07.035_ +_Adam A. Atanas, Jungsoo Kim, Ziyu Wang, Eric Bueno, McCoy Becker, Di Kang, Jungyeon Park, Talya S. Kramer, Flossie K. Wan, Saba Baskoylu, Ugur Dag, Elpiniki Kalogeropoulou, Matthew A. Gomes, Cassi Estrem, Netta Cohen, Vikash K. Mansinghka, and Steven W. Flavell_ + +_Cell, Volume 186, Issue 19, 2023, Pages 4134-4151.e31, ISSN 0092-8674_
_Published: September 14, 2023 https://doi.org/10.1016/j.cell.2023.07.035_ - For quantitative analaysis, the two adult datasets from Witvliet et al were averaged. (https://www.nature.com/articles/s41586-021-03778-8) - Self looping and single synapse edges were excluded From 6ca6a4001c26182d0ccba7217df0e703695030f8 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:20:25 +0100 Subject: [PATCH 47/80] Update Beets_2023.md --- docs/Beets_2023.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/docs/Beets_2023.md b/docs/Beets_2023.md index fb717fcf..5c8d359e 100644 --- a/docs/Beets_2023.md +++ b/docs/Beets_2023.md @@ -1,6 +1,11 @@ ## System-wide mapping of peptide-GPCR interactions in C. elegans _Beets I, Zels S, Vandewyer E, Demeulemeester J, Caers J, Baytemur E, Courtney A, Golinelli L, Hasakioğulları İ, Schafer WR, Vértes PE, Mirabeau O, Schoofs L._ -_doi: 10.1016/j.celrep.2023.113058_ +_Cell Reports, +Volume 42, Issue 9, +2023, +113058, +ISSN 2211-1247, +
https://doi.org/10.1016/j.celrep.2023.113058_ - They report a genome-wide peptide-GPCR interaction map in _C.elegans_ From bf5b59670e5ff8d93a8c7f8061ef165032e756a8 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:22:47 +0100 Subject: [PATCH 48/80] Update Bentley_2016.md --- docs/Bentley_2016.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/docs/Bentley_2016.md b/docs/Bentley_2016.md index 0605cce6..d3b3b158 100644 --- a/docs/Bentley_2016.md +++ b/docs/Bentley_2016.md @@ -1,8 +1,6 @@ ## The Multilayer Connectome of Caenorhabditis elegans -*Barry Bentley, Robyn Branicky, Christopher L. Barnes, Yee Lian Chew, Eviatar Yemini, Edward T. Bullmore, Petra E. Vértes , William R. Schafer* +*Barry Bentley, Robyn Branicky, Christopher L. Barnes, Yee Lian Chew, Eviatar Yemini, Edward T. Bullmore, Petra E. Vértes , William R. Schafer*
*Published: December 16, 2016*
*Citation: Bentley B, Branicky R, Barnes CL, Chew YL, Yemini E, Bullmore ET, et al. (2016) The Multilayer Connectome of Caenorhabditis elegans. PLoS Comput Biol 12(12): e1005283. https://doi.org/10.1371/journal.pcbi.1005283* -*Published: December 16, 2016 -https://doi.org/10.1371/journal.pcbi.1005283* **Abstract:** - Extrasynaptic modulation (monoamines and peptides) influence neural circuits From b988e2575e7467f962c12c64cf77c2e45ecfa7f0 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:23:16 +0100 Subject: [PATCH 49/80] Update Bentley_2016.md --- docs/Bentley_2016.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Bentley_2016.md b/docs/Bentley_2016.md index d3b3b158..9ff3ffcd 100644 --- a/docs/Bentley_2016.md +++ b/docs/Bentley_2016.md @@ -1,5 +1,5 @@ ## The Multilayer Connectome of Caenorhabditis elegans -*Barry Bentley, Robyn Branicky, Christopher L. Barnes, Yee Lian Chew, Eviatar Yemini, Edward T. Bullmore, Petra E. Vértes , William R. Schafer*
*Published: December 16, 2016*
*Citation: Bentley B, Branicky R, Barnes CL, Chew YL, Yemini E, Bullmore ET, et al. (2016) The Multilayer Connectome of Caenorhabditis elegans. PLoS Comput Biol 12(12): e1005283. https://doi.org/10.1371/journal.pcbi.1005283* +*Barry Bentley, Robyn Branicky, Christopher L. Barnes, Yee Lian Chew, Eviatar Yemini, Edward T. Bullmore, Petra E. Vértes , William R. Schafer*
*Published: December 16, 2016*
*PLoS Comput Biol 12(12): e1005283. https://doi.org/10.1371/journal.pcbi.1005283* **Abstract:** From 2b00be04c00061f59b2f3b8f166e107c98009eb8 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:24:02 +0100 Subject: [PATCH 50/80] Update Brittin_2021.md --- docs/Brittin_2021.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Brittin_2021.md b/docs/Brittin_2021.md index 1f084d73..da98adeb 100644 --- a/docs/Brittin_2021.md +++ b/docs/Brittin_2021.md @@ -1,5 +1,5 @@ ## A multi-scale brain map derived from whole-brain volumetric reconstructions -_Brittin, C.A., Cook, S.J., Hall, D.H. et al_ +_Brittin, C.A., Cook, S.J., Hall, D.H. et al_
_Nature 591, 105–110_ _Published: 24 February 2021 https://doi.org/10.1038/s41586-021-03284-x_ From b2269b696a5a5f17da7fbbac8b65bb0108f12aa0 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:25:22 +0100 Subject: [PATCH 51/80] Update Cook_2019.md --- docs/Cook_2019.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/Cook_2019.md b/docs/Cook_2019.md index d0c8ddaf..058891f4 100644 --- a/docs/Cook_2019.md +++ b/docs/Cook_2019.md @@ -1,7 +1,6 @@ ## Whole-animal connectomes of both _Caeonrhabditis elegans_ sexes -_Steven J. Cook, Travis A. Jarrell, Christopher A. Brittin, Yi Wang, Adam E. Bloniarz, Maksim A. Yakovlev, Ken C. Q. Nguyen, Leo T.-H. Tang, Emily A. Bayer, Janet S. Duerr, Hannes E. Bülow, Oliver Hobert, David H. Hall & Scott W. Emmons_ +_Steven J. Cook, Travis A. Jarrell, Christopher A. Brittin, Yi Wang, Adam E. Bloniarz, Maksim A. Yakovlev, Ken C. Q. Nguyen, Leo T.-H. Tang, Emily A. Bayer, Janet S. Duerr, Hannes E. Bülow, Oliver Hobert, David H. Hall & Scott W. Emmons_
_Nature 571, 63–71
Published: 3 July 2019 https://doi.org/10.1038/s41586-019-1352-7_ -_Published: 3 July 2019_ # Abstract - Present quantitative connectivity matrices that encompass all connections from sensory input to end-organ output across the entire animal. From 9d97d9b2d5a66564ceef362077e0f3b4638531c0 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:25:36 +0100 Subject: [PATCH 52/80] Update Cook_2019.md --- docs/Cook_2019.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/Cook_2019.md b/docs/Cook_2019.md index 058891f4..acac4752 100644 --- a/docs/Cook_2019.md +++ b/docs/Cook_2019.md @@ -1,5 +1,7 @@ ## Whole-animal connectomes of both _Caeonrhabditis elegans_ sexes -_Steven J. Cook, Travis A. Jarrell, Christopher A. Brittin, Yi Wang, Adam E. Bloniarz, Maksim A. Yakovlev, Ken C. Q. Nguyen, Leo T.-H. Tang, Emily A. Bayer, Janet S. Duerr, Hannes E. Bülow, Oliver Hobert, David H. Hall & Scott W. Emmons_
_Nature 571, 63–71
Published: 3 July 2019 https://doi.org/10.1038/s41586-019-1352-7_ +_Steven J. Cook, Travis A. Jarrell, Christopher A. Brittin, Yi Wang, Adam E. Bloniarz, Maksim A. Yakovlev, Ken C. Q. Nguyen, Leo T.-H. Tang, Emily A. Bayer, Janet S. Duerr, Hannes E. Bülow, Oliver Hobert, David H. Hall & Scott W. Emmons_ + +_Nature 571, 63–71
Published: 3 July 2019 https://doi.org/10.1038/s41586-019-1352-7_ # Abstract From 3c236bcbdfde2b07d005d21e3bd0214dda2a9b5d Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:27:19 +0100 Subject: [PATCH 53/80] Update Cook_2020.md --- docs/Cook_2020.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Cook_2020.md b/docs/Cook_2020.md index 65c6ea0a..ee0be99f 100644 --- a/docs/Cook_2020.md +++ b/docs/Cook_2020.md @@ -1,5 +1,5 @@ ## The connectome of the Caenorhabditis elegans pharynx -_Steven J. Cook, Charles M. Crouse, Eviatar Yemini, David H. Hall, Scott W. Emmons, Oliver Hobert_ - +_Steven J. Cook, Charles M. Crouse, Eviatar Yemini, David H. Hall, Scott W. Emmons, Oliver Hobert_
+_J Comp Neurol. 2020; 528: 2767–2784_
_First published: 30 April 2020 https://doi.org/10.1002/cne.24932_ From 58fe361a4f37dfdab67e92c2b8d6c140334394e4 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:27:57 +0100 Subject: [PATCH 54/80] Update Dag_2023.md --- docs/Dag_2023.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/docs/Dag_2023.md b/docs/Dag_2023.md index f389eff8..5bb78cea 100644 --- a/docs/Dag_2023.md +++ b/docs/Dag_2023.md @@ -1,7 +1,5 @@ ## Dissecting the functional organization of the C. elegans serotonergic system at whole-brain scale -_Ugur Dag, Ijeoma Nwabudike, Di Kang, Matthew A. Gomes, Jungsoo Kim, Adam A. Atanas, Eric Bueno, Cassi Estrem, Sarah Pugliese, Ziyu Wang, Emma Towlson, Steven W. Flavell, -Dissecting the functional organization of the C. elegans serotonergic system at whole-brain scale_ - +_Ugur Dag, Ijeoma Nwabudike, Di Kang, Matthew A. Gomes, Jungsoo Kim, Adam A. Atanas, Eric Bueno, Cassi Estrem, Sarah Pugliese, Ziyu Wang, Emma Towlson, Steven W. Flavell_
_Cell, Volume 186, Issue 12, 2023, From 6b8472c068ee02e7f285d5b07a426a026591cda7 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:29:54 +0100 Subject: [PATCH 55/80] Update Fenyves_2020.md --- docs/Fenyves_2020.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/Fenyves_2020.md b/docs/Fenyves_2020.md index faed81f8..8bfdb21e 100644 --- a/docs/Fenyves_2020.md +++ b/docs/Fenyves_2020.md @@ -1,7 +1,9 @@ ## Synaptic polarity and sign-balance prediction using gene expression data in the Caenorhabditis elegans chemical synapse neuronal connectome network -_Bánk G. Fenyves, Gábor S. Szilágyi, Zsolt Vassy, Csaba Sőti, Peter Csermely +_Bánk G. Fenyves, Gábor S. Szilágyi, Zsolt Vassy, Csaba Sőti, Peter Csermely
+ *PLOS Computational Biology 16(12): e1007974*
Published: December 21, 2020 https://doi.org/10.1371/journal.pcbi.1007974_ +**Summary** - Present a gene expression-based sign prediction of the ionotropic chemical synapse connectome of _C.elegans_ - They have an open source tool (http://elegansign.linkgroup.hu) that uses three differene connectomes: WormWiring; Cook et al.; Varshney et al. From 493578189154f27e92296af255ee363a4f4cecad Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:30:48 +0100 Subject: [PATCH 56/80] Update Gendrel_2016.md --- docs/Gendrel_2016.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/Gendrel_2016.md b/docs/Gendrel_2016.md index e7cd8864..a2626c4e 100644 --- a/docs/Gendrel_2016.md +++ b/docs/Gendrel_2016.md @@ -1 +1,2 @@ ## A cellular and regulatory map of the GABAergic nervous system of C. elegans +_Gendrel M, Atlas EG, Hobert O
Elife. 2016 Oct 14;5:e17686.
doi: 10.7554/eLife.17686. PMID: 27740909; PMCID: PMC5065314_ From 0c18117aa7733848961f9d45598b536d077299f5 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:31:43 +0100 Subject: [PATCH 57/80] Update Gendrel_2016.md --- docs/Gendrel_2016.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Gendrel_2016.md b/docs/Gendrel_2016.md index a2626c4e..7201880e 100644 --- a/docs/Gendrel_2016.md +++ b/docs/Gendrel_2016.md @@ -1,2 +1,2 @@ ## A cellular and regulatory map of the GABAergic nervous system of C. elegans -_Gendrel M, Atlas EG, Hobert O
Elife. 2016 Oct 14;5:e17686.
doi: 10.7554/eLife.17686. PMID: 27740909; PMCID: PMC5065314_ +_Gendrel M, Atlas EG, Hobert O
Elife. 2016 Oct 14;5:e17686.
Published: 14 October 2016 https://doi.org/10.7554/eLife.17686_ From 7a38c66ae665791f6d45660a3bf3a9dca222294e Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:32:13 +0100 Subject: [PATCH 58/80] Update Gendrel_2016.md --- docs/Gendrel_2016.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Gendrel_2016.md b/docs/Gendrel_2016.md index 7201880e..4a02b67e 100644 --- a/docs/Gendrel_2016.md +++ b/docs/Gendrel_2016.md @@ -1,2 +1,2 @@ ## A cellular and regulatory map of the GABAergic nervous system of C. elegans -_Gendrel M, Atlas EG, Hobert O
Elife. 2016 Oct 14;5:e17686.
Published: 14 October 2016 https://doi.org/10.7554/eLife.17686_ +_Gendrel M, Atlas EG, Hobert O
Elife
Published: 14 October 2016 https://doi.org/10.7554/eLife.17686_ From 10be3ff1f6bc0661744bed5f9c690035a1a1c52a Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:33:25 +0100 Subject: [PATCH 59/80] Update Hall_1991.md --- docs/Hall_1991.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/Hall_1991.md b/docs/Hall_1991.md index 8cc5c2ab..72a5d799 100644 --- a/docs/Hall_1991.md +++ b/docs/Hall_1991.md @@ -1,3 +1,4 @@ ## The Posterior Nervous System of the Nematode Caenorhabditis elegans: Serial Reconstruction of Identified Neurons and Complete Pattern of Synaptic Interactions -_David H. Hall and Richard L. Russell_ +_David H. Hall and Richard L. Russell_
+*Journal of Neuroscience 1 January 1991, 11 (1) 1-22; DOI: 10.1523/JNEUROSCI.11-01-00001.1991* From 7e805a15bafc394ebae4affd0017c0fed621ec7f Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:33:45 +0100 Subject: [PATCH 60/80] Update Hall_1991.md --- docs/Hall_1991.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Hall_1991.md b/docs/Hall_1991.md index 72a5d799..c4c77dde 100644 --- a/docs/Hall_1991.md +++ b/docs/Hall_1991.md @@ -1,4 +1,4 @@ ## The Posterior Nervous System of the Nematode Caenorhabditis elegans: Serial Reconstruction of Identified Neurons and Complete Pattern of Synaptic Interactions _David H. Hall and Richard L. Russell_
-*Journal of Neuroscience 1 January 1991, 11 (1) 1-22; DOI: 10.1523/JNEUROSCI.11-01-00001.1991* +*Journal of Neuroscience
1 January 1991, 11 (1) 1-22; DOI: 10.1523/JNEUROSCI.11-01-00001.1991* From bad9f33edaa08073b3d5cc5a6b9fbfcbf230d05f Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:34:29 +0100 Subject: [PATCH 61/80] Update Pereira_2015.md --- docs/Pereira_2015.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Pereira_2015.md b/docs/Pereira_2015.md index e1fcc502..ab1c276b 100644 --- a/docs/Pereira_2015.md +++ b/docs/Pereira_2015.md @@ -1,6 +1,6 @@ ## A cellular and regulatory map of the cholinergic nervous system of C. elegans -_Laura Pereira, Paschalis Kratsios, Esther Serrano-Saiz, Hila Sheftel, Avi E Mayo, David H Hall, John G White, Brigitte LeBoeuf, L Rene Garcia, Uri Alon, and Oliver Hobert_ - +_Laura Pereira, Paschalis Kratsios, Esther Serrano-Saiz, Hila Sheftel, Avi E Mayo, David H Hall, John G White, Brigitte LeBoeuf, L Rene Garcia, Uri Alon, and Oliver Hobert_
+*eLife* _Published: 25 December 2015 https://doi.org/10.7554/eLife.12432.001_ From 367ddb6f24bb6540ab7109c2b44b600b3f4e46c2 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:34:38 +0100 Subject: [PATCH 62/80] Update Pereira_2015.md --- docs/Pereira_2015.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Pereira_2015.md b/docs/Pereira_2015.md index ab1c276b..8dbcc5b4 100644 --- a/docs/Pereira_2015.md +++ b/docs/Pereira_2015.md @@ -1,6 +1,6 @@ ## A cellular and regulatory map of the cholinergic nervous system of C. elegans _Laura Pereira, Paschalis Kratsios, Esther Serrano-Saiz, Hila Sheftel, Avi E Mayo, David H Hall, John G White, Brigitte LeBoeuf, L Rene Garcia, Uri Alon, and Oliver Hobert_
-*eLife* +*eLife*
_Published: 25 December 2015 https://doi.org/10.7554/eLife.12432.001_ From ddb322ab3b00b06a876d87966dba1a6187931854 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:34:48 +0100 Subject: [PATCH 63/80] Update Pereira_2015.md --- docs/Pereira_2015.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/Pereira_2015.md b/docs/Pereira_2015.md index 8dbcc5b4..68d364c5 100644 --- a/docs/Pereira_2015.md +++ b/docs/Pereira_2015.md @@ -1,5 +1,6 @@ ## A cellular and regulatory map of the cholinergic nervous system of C. elegans -_Laura Pereira, Paschalis Kratsios, Esther Serrano-Saiz, Hila Sheftel, Avi E Mayo, David H Hall, John G White, Brigitte LeBoeuf, L Rene Garcia, Uri Alon, and Oliver Hobert_
+_Laura Pereira, Paschalis Kratsios, Esther Serrano-Saiz, Hila Sheftel, Avi E Mayo, David H Hall, John G White, Brigitte LeBoeuf, L Rene Garcia, Uri Alon, and Oliver Hobert_ + *eLife*
_Published: 25 December 2015 https://doi.org/10.7554/eLife.12432.001_ From 2ad67a23d0b6dc01612128d41e6431474523c80e Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:36:49 +0100 Subject: [PATCH 64/80] Update Randi_2023.md --- docs/Randi_2023.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/Randi_2023.md b/docs/Randi_2023.md index 8f377905..a5c3ef5e 100644 --- a/docs/Randi_2023.md +++ b/docs/Randi_2023.md @@ -1 +1,4 @@ ## Neural signal propagation atlas of Caenorhabditis elegans +_Randi, F., Sharma, A.K., Dvali, S., Leifer, M.
Nature 623, 406–414 (2023) https://doi.org/10.1038/s41586-023-06683-4_ + +**Summary** From 10fb371db295ffdbd27b382876cf17e9a9ba1fc6 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:38:19 +0100 Subject: [PATCH 65/80] Update Ripoll_2023.md --- docs/Ripoll_2023.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/docs/Ripoll_2023.md b/docs/Ripoll_2023.md index 0c373ab3..df37c26b 100644 --- a/docs/Ripoll_2023.md +++ b/docs/Ripoll_2023.md @@ -1 +1,8 @@ ## The neuropeptidergic connectome of C. elegans +*Ripoll-Sánchez L, Watteyne J, Sun H, Fernandez R, Taylor SR, Weinreb A, Bentley BL, Hammarlund M, Miller DM 3rd, Hobert O, Beets I, Vértes PE, Schafer WR.*
+Neuron, +Volume 111, Issue 22, +2023, +Pages 3570-3589.e5, +ISSN 0896-6273, +https://doi.org/10.1016/j.neuron.2023.09.043.* From 09e76b5601cab76ca77906fe2f383cb3ccce23f6 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:38:28 +0100 Subject: [PATCH 66/80] Update Ripoll_2023.md --- docs/Ripoll_2023.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Ripoll_2023.md b/docs/Ripoll_2023.md index df37c26b..abb1a568 100644 --- a/docs/Ripoll_2023.md +++ b/docs/Ripoll_2023.md @@ -1,6 +1,6 @@ ## The neuropeptidergic connectome of C. elegans *Ripoll-Sánchez L, Watteyne J, Sun H, Fernandez R, Taylor SR, Weinreb A, Bentley BL, Hammarlund M, Miller DM 3rd, Hobert O, Beets I, Vértes PE, Schafer WR.*
-Neuron, +*Neuron, Volume 111, Issue 22, 2023, Pages 3570-3589.e5, From 3263a6169f01544ba04035b70760bfbd9d2b1581 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:39:33 +0100 Subject: [PATCH 67/80] Update Serrano_2013.md --- docs/Serrano_2013.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/docs/Serrano_2013.md b/docs/Serrano_2013.md index bd1b381d..21fd832d 100644 --- a/docs/Serrano_2013.md +++ b/docs/Serrano_2013.md @@ -1 +1,8 @@ ## Modular control of glutamatergic neuronal identity in C. elegans by distinct homeodomain proteins +_Serrano-Saiz E, Poole RJ, Felton T, Zhang F, De La Cruz ED, Hobert O._
+*Cell, +Volume 155, Issue 3, +2013, +Pages 659-673, +ISSN 0092-8674, +https://doi.org/10.1016/j.cell.2013.09.052.* From 247ae03bb0515b179c0f1bd61f5280d038c5b8b3 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:40:22 +0100 Subject: [PATCH 68/80] Update Taylor_2021.md --- docs/Taylor_2021.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/Taylor_2021.md b/docs/Taylor_2021.md index 508db148..9ae72a99 100644 --- a/docs/Taylor_2021.md +++ b/docs/Taylor_2021.md @@ -1,8 +1,14 @@ ## Molecular topography of an entire nervous system _Seth R. Taylor, Gabriel Santpere, Alexis Weinreb, Marc Hammarlund, Oliver Hobert, David M. Miller_ +*Cell, +Volume 184, Issue 16, +2021, +Pages 4329-4347.e23, +ISSN 0092-8674,* _Published: July 07, 2021 DOI:https://doi.org/10.1016/j.cell.2021.06.023_ +**Summary** - Gene expression profiles of all 118 neuron classes in the _C.elegans_ hermaphrodite - Each neuron type expresses a distinct code of neuropeptide genes and receptors - Expression profiles enable discovery of cell-type-specific _cis_-regulatory sequences From 881c335606ed978f89a05aa558dc2a9f7fb8412b Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:40:36 +0100 Subject: [PATCH 69/80] Update Taylor_2021.md --- docs/Taylor_2021.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Taylor_2021.md b/docs/Taylor_2021.md index 9ae72a99..35d26225 100644 --- a/docs/Taylor_2021.md +++ b/docs/Taylor_2021.md @@ -5,7 +5,7 @@ Volume 184, Issue 16, 2021, Pages 4329-4347.e23, -ISSN 0092-8674,* +ISSN 0092-8674,*
_Published: July 07, 2021 DOI:https://doi.org/10.1016/j.cell.2021.06.023_ **Summary** From 2ed6f53daec44477edf99de3bfd552f18736e2c7 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:41:25 +0100 Subject: [PATCH 70/80] Update Varshney_2011.md --- docs/Varshney_2011.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/Varshney_2011.md b/docs/Varshney_2011.md index 613e24ee..bec7d03d 100644 --- a/docs/Varshney_2011.md +++ b/docs/Varshney_2011.md @@ -1,6 +1,7 @@ ## Structural Properties of the Caenorhabditis elegans Neuronal Network _Lav R. Varshney, Beth L. Chen, Eric Paniagua, David H. Hall, Dmitri B. Chklovskii_ +*PLOS Computational Biology 7(2): e1001066*
_Published: February 3, 2011 (https://doi.org/10.1371/journal.pcbi.1001066)_ From 6d0a2bb3d75800c69b6f69f2b5998d9a568525e9 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:42:14 +0100 Subject: [PATCH 71/80] Update White_1986.md --- docs/White_1986.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/White_1986.md b/docs/White_1986.md index ee414b1b..8b0a67be 100644 --- a/docs/White_1986.md +++ b/docs/White_1986.md @@ -2,6 +2,7 @@ *By J.G.White, E.Southgate, J.N. Thomson and S.Brenner, F.R.S.* +*Phil. Trans. R. Soc. Lond. B3141–340*
*Published 12 November 1986* **Type of Connectomics Data** From 1b260c79ba5f2c5508f4a1086e68d67f7732ed15 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:42:56 +0100 Subject: [PATCH 72/80] Update Witvliet_2021.md --- docs/Witvliet_2021.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/Witvliet_2021.md b/docs/Witvliet_2021.md index 750c0996..94e5370d 100644 --- a/docs/Witvliet_2021.md +++ b/docs/Witvliet_2021.md @@ -1,6 +1,7 @@ ## Connectomes across development reveal principles of brain maturation _Witvliet, D., Mulcahy, B., Mitchell, J.K. et al_ +*Nature 596, 257–261*
_Published: 4 August 2021 (https://doi.org/10.1038/s41586-021-03778-8)_ www.nemanode.org From 20ce021a61c7e91647bb087fce9fcabf57646811 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:43:57 +0100 Subject: [PATCH 73/80] Update Yemini_2021.md --- docs/Yemini_2021.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/Yemini_2021.md b/docs/Yemini_2021.md index 405c0074..5f584cee 100644 --- a/docs/Yemini_2021.md +++ b/docs/Yemini_2021.md @@ -1,7 +1,9 @@ ## NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans _Eviatar Yemini, Albert Lin , Amin Nejatbakhsh , Erdem Varol , Ruoxi Sun, Gonzalo E Mena, Aravinthan D T Samuel, Liam Paninski, Vivek Venkatachalam, Oliver Hobert_ -_DOI: 10.1016/j.cell.2020.12.012_ + +*Cell. 2021 Jan 7;184(1):272-288.e11*
+*https://doi.org/10.1016/j.cell.2020.12.012* - Identified brainwide expression patterns of all metabotropic receptors for ACh, GABA, and Glu completing a map of this communication network - Uncover changes in cell fate caused by TF mutations From 4c7202dad8e5c83e260603adf2318a8aacb755ec Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:44:13 +0100 Subject: [PATCH 74/80] Update Yemini_2021.md --- docs/Yemini_2021.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/Yemini_2021.md b/docs/Yemini_2021.md index 5f584cee..f7c799a1 100644 --- a/docs/Yemini_2021.md +++ b/docs/Yemini_2021.md @@ -5,6 +5,7 @@ *Cell. 2021 Jan 7;184(1):272-288.e11*
*https://doi.org/10.1016/j.cell.2020.12.012* +**Summary** - Identified brainwide expression patterns of all metabotropic receptors for ACh, GABA, and Glu completing a map of this communication network - Uncover changes in cell fate caused by TF mutations - Record brainwide activity in response to attractive and repulsive chemosensory cues, characterizing multimodal coding for these stimuli From 4c67610d8c559b52d5429ce1b899bd0d2c5d2325 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:49:26 +0100 Subject: [PATCH 75/80] Update Cook_2020.md --- docs/Cook_2020.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Cook_2020.md b/docs/Cook_2020.md index ee0be99f..ac3604b4 100644 --- a/docs/Cook_2020.md +++ b/docs/Cook_2020.md @@ -1,4 +1,4 @@ - ## The connectome of the Caenorhabditis elegans pharynx +## The connectome of the Caenorhabditis elegans pharynx _Steven J. Cook, Charles M. Crouse, Eviatar Yemini, David H. Hall, Scott W. Emmons, Oliver Hobert_
_J Comp Neurol. 2020; 528: 2767–2784_
From 1422358e4e7eb538844b503cc616b115264a66b4 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:50:35 +0100 Subject: [PATCH 76/80] Update Cook_2019.md --- docs/Cook_2019.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Cook_2019.md b/docs/Cook_2019.md index acac4752..6546a906 100644 --- a/docs/Cook_2019.md +++ b/docs/Cook_2019.md @@ -1,10 +1,10 @@ -## Whole-animal connectomes of both _Caeonrhabditis elegans_ sexes +# Whole-animal connectomes of both _Caeonrhabditis elegans_ sexes _Steven J. Cook, Travis A. Jarrell, Christopher A. Brittin, Yi Wang, Adam E. Bloniarz, Maksim A. Yakovlev, Ken C. Q. Nguyen, Leo T.-H. Tang, Emily A. Bayer, Janet S. Duerr, Hannes E. Bülow, Oliver Hobert, David H. Hall & Scott W. Emmons_ _Nature 571, 63–71
Published: 3 July 2019 https://doi.org/10.1038/s41586-019-1352-7_ -# Abstract +## Abstract - Present quantitative connectivity matrices that encompass all connections from sensory input to end-organ output across the entire animal. - Serial EM reconstructions that are based on analysis of both new and previously published EM update results and include data on male head - Nervous system differs between sexes at multiple levels: From 87526d025ecfe3a95c9ab51bf8df6fc884679654 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 16:54:02 +0100 Subject: [PATCH 77/80] Update Cook_2019.md --- docs/Cook_2019.md | 38 ++++++++++---------------------------- 1 file changed, 10 insertions(+), 28 deletions(-) diff --git a/docs/Cook_2019.md b/docs/Cook_2019.md index 6546a906..a6ee623d 100644 --- a/docs/Cook_2019.md +++ b/docs/Cook_2019.md @@ -12,7 +12,7 @@ _Nature 571, 63–71
Published: 3 July 2019 https://doi.org/10.1038/s41586-0 - Inputs from sex-specific circuitry to central circuitry reveal points at which sexual and non-sexual pathways converge - Sex-shared central pathways, a substantial no. of connections differ in strength between the sexes -**Whole animal connectomes** +### Whole animal connectomes - Small world, network motifs, modules and rich clubs - Reconstruction of circuity for the male head, including the nerve ring and retrovesicular ganglion, from a new EM series and re-annotate previously generated prints of the hermaphrodite - Graph of the hermaphrodite connectome has 460 nodes (302 neurons, 132 muscles and 26 non-muscle end organs) @@ -21,7 +21,7 @@ _Nature 571, 63–71
Published: 3 July 2019 https://doi.org/10.1038/s41586-0 - Small number (1-5) of synaptic steps between the sensory neurons and the end organs and feedforward nature of the networks - Placement of the nodes to the neuroanatomy of the worm reflects economical wiring, a property commonly found for nervous systems, including in C.elegans -**Architecture of information flow** +### Architecture of information flow - Polarity of the chemical synapses and the architecture of the physical connectivity networks to order the sex-shared neurons and end organ classes using an algorithm that detects hierarchy in a network - Interneurons can be categorised roughly into one of three layers that reflect preponderance of their output onto the layer below and approx the number of synaptic steps to motor neurons - Fourth interneuron category: consists of interneurons that interact across all layers, cannot be fitted into this layered structure @@ -33,7 +33,7 @@ _Nature 571, 63–71
Published: 3 July 2019 https://doi.org/10.1038/s41586-0 - Node degree: amount of convergence and divergence at single nodes in a network (number of attached edges) - Diverging connectivity enables information from single sensory neurons to potentially reach from 70% to 98% of all the other cells in the network within two synaptic steps -**Generation of body movements** +### Generation of body movements - Postural movements of C.elegans during foraging and locomotion are generated by a set of 95 body wall muscles that are arranged in four longitudinal rows, two of which are sub-dorsal and the other two are sub-ventral - Within each of these quadrants, adjacent muscle cells are electrically coupled by gap junctions - 154 neurons in 46 classes have NMJs with these somatic muscles @@ -46,21 +46,21 @@ _Nature 571, 63–71
Published: 3 July 2019 https://doi.org/10.1038/s41586-0 - Third is a general body curvature, corresponding to the potential effect of the sublateral motor neurons - Fourth includes head bending, corresponding to the head motor neurons -**Reproducibility of connectivity** +### Reproducibility of connectivity - Left-right homologous neuron pairs onto left-right homologous targets in the nerve ring of the hermaphrodite reconstruction to assess the amount of natural variability in connectivity - For chemical connections, edge weights varied by 10-40%, depending on connection strength - In both sexes, the gustatory neurons ASEL (left neuron of the pair) has greater chemical than the ASER (right neuron of the pair) to the olfactory neuron class AWC. - Known to be lateralized in its ability to sense chemosensory cues - We confirmed the difference in connectivity by in vivo fluorescence labelling of this synaptic connection -**Comparison of the sexes** +### Comparison of the sexes - Circuits controlling the sex-unique behaviours of egg laying and copulation include both sex-specific and sex-shared neurons, - Most notable in the male, in which the neural network that controls copulation consists of 85 male-specific and 64 shared neurons - Sex-specific neurons connect into the sex-shared central circuity in the head with 2 functions - Regulate behaviour during overt reproductive activity - Mediate sex specific appetitive decision making -**Discussion** +## Discussion - Physical connectivity matrices for the entire nervous system of an animal for both adult sexes - Amount of convergence and divergence of sensory input pathways is such that particular behavioural response pathways cannot be readily identified in general - Major motor neurons and primary premotor interneurons are highly interconnected @@ -72,22 +72,11 @@ _Nature 571, 63–71
Published: 3 July 2019 https://doi.org/10.1038/s41586-0 - C.elegans neurons are isopotential, properties of these neurons may be compartmentalised and signalling may not be uniform or simultaneous at all synapses - Modelling the functions of the nervous system at the abstracted level of the connectivity network cannot be seriously cannot be seriously undertaken if a considerable number of nodes and edges are missing -**Methods** -- Adjacency matrices: data from neuron maps are abstracted as an adjacency matrix with weights that indicate the total amount of physical connectivity between each cell pair - - - - - - - - - -## Significant updates and corrections to previous data (Whole-animal connectome) -- DVB/PVT mixup. The ventral cord processes of these neurons were crossed in MOW. PVT extends to the head, DVB ends mid-body. Previously reported: (WBG 16(1):24 (October 1, 1999)). +## Significant updates and corrections to previous data +- DVB/PVT mixup. The ventral cord processes of these neurons were crossed in MOW. PVT extends to the head, DVB ends mid-body. - PVCL and PVCR. In MOW these were switched at N2U ventral cord section 1656. - Sublateral motor neurons. MOW contained no data for the sublateral cords anterior or posterior to the nerve ring, and no neuromuscular junctions for these neurons along the body. Synapses were first noted by immunofluorescence, then confirmed by sampling multiple animals (not reconstructed). -- Lateral nerves were closely examined in multiple animals to assess synapses for the first time (not reconstructed except for short portions) (Ramirez-Suarez N.J., Belalcazar H.M., Salazar C.J., Beyaz B., Raja B., Nguyen K.C.Q., Celestrin K., Fredens J., Færgeman N.J., Hall D.H., and Bülow H.E. (2018) Axon-dependent patterning and maintenance of somatosensory dendritic arbors, Dev Cell. 2019 Jan 28;48(2):229-244.). +- Lateral nerves were closely examined in multiple animals to assess synapses for the first time (not reconstructed except for short portions) - Motor neurons re-assigned as interneurons: RIM, RMF, RMG. nmj's reported in MOW for the adult RMF could not be verified. - Interneurons reassigned as motor neurons: SAB, SIA, SIB. - Interneuron reasssigned as sensory neuron: DVA. @@ -95,11 +84,4 @@ _Nature 571, 63–71
Published: 3 July 2019 https://doi.org/10.1038/s41586-0 - Synapses to hypodermis, both chemical and gap junctional, were occasionally reported in MOW but were not systematically scored until now. - Extensive gap junctional connectivity of hmc (head mesodermal cell) to muscle was previously noted (MRC notebooks) but never systematically assessed and reported. - PDB is considered to be an AS class motor neuron (AS12). It shares all the characteristics of the other members of this class, except the route taken by its commissure differs by going first posteriorly before crossing the body and progressing anteriorly (the reason behind its unique name, J. White, personal communication). In the male it has an extensive dendritic arbor involved in mating circuitry, as does AS11. -- Muscle arms of the bodywall muscles of the head (#1-8) were traced to their NMJ inputs for the first time - -**Male-specific neurons** -- There are two new classes of male-specific neurons: MCM (L and R) are interneurons in the head (Sammut et al. 2015, Nature 526, 385-390); PHD (L and R) are putative sensory neurons in the tail derived during the L4 larval stage by transdifferentiation of the phasmid socket cell PHso1 (Sulston et al., 1980; Molina-Garcia et al., https://www.biorxiv.org/content/early/2018/03/21/285320). -- In Jarrell et al., the processes of PHD(L/R) were misidentified as branches of R8B. -- In Jarrell et al., LUA and PHC were reversed. Connectivity data given for LUA is in fact due to PHC, and vice versa. -- AN3 of Jarrell et al. is AVF (verified by transgene expression of a synaptic marker (unpublished observations)). AN3 was one of three interneuron processes of neurons with cell bodies in the head that could not be positiviely identified in the pre-anal ganglion. -- The other two, AN1 and AN2, are tentatively assigned as AVH and AVJ, respectively. +- Muscle arms of the bodywall muscles of the head (#1-8) were traced to their NMJ inputs for the first time. From f0701a929f951556cd6fce8b4a02107006bc15ff Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 17:06:22 +0100 Subject: [PATCH 78/80] Update Timeline.md --- docs/Timeline.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/Timeline.md b/docs/Timeline.md index 180d8337..f820f0cc 100644 --- a/docs/Timeline.md +++ b/docs/Timeline.md @@ -26,7 +26,7 @@ flowchart TD end subgraph 2020-2030 - J[Brittin et al. 2021]:::anat & K[Witvliet et al. 2021]:::anat & L[Taylor et al. 2021]:::gene & M[Yemini et al. 2021]:::gene & N[Beets et al. 2023]:::gene & P[Randi et al. 2023]:::func & NP[Ripoll-Sanchez et al. 2023]:::es + J[Brittin et al. 2021]:::anat & K[Witvliet et al. 2021]:::anat & L[Taylor et al. 2021]:::gene & M[Yemini et al. 2021]:::gene & N[Beets et al. 2023]:::gene & P[Randi et al. 2023]:::func & NP[Ripoll-Sanchez et al. 2023]:::es & R[Dag et al. 2023]:::func & T[Atanas et al. 2023]:::func end @@ -61,4 +61,8 @@ flowchart TD K --> P NP --> P F --> P + M --> R + T --> R + A --> R + K --> R ``` From c5706daa68eb6e351717d8430f7cdd82697e6bc0 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 17:08:01 +0100 Subject: [PATCH 79/80] Update Timeline.md --- docs/Timeline.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Timeline.md b/docs/Timeline.md index f820f0cc..92e0b4ef 100644 --- a/docs/Timeline.md +++ b/docs/Timeline.md @@ -7,7 +7,7 @@ flowchart TD subgraph 1970-1980 - A1[Albertson & Thomson 1976]:::anat + A1[Albertson & Thomson 1976]:::anat end subgraph 1980-1990 A[White et al. 1986]:::anat & B[Durbin 1987]:::anat From ac72e24d8f55922b8a392e0d492bcc6e1c2e7801 Mon Sep 17 00:00:00 2001 From: yasinthanvickneswaran <147663006+yasinthanvickneswaran@users.noreply.github.com> Date: Mon, 17 Jun 2024 17:09:31 +0100 Subject: [PATCH 80/80] Update Timeline.md --- docs/Timeline.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Timeline.md b/docs/Timeline.md index 92e0b4ef..4dcf0a51 100644 --- a/docs/Timeline.md +++ b/docs/Timeline.md @@ -7,7 +7,7 @@ flowchart TD subgraph 1970-1980 - A1[Albertson & Thomson 1976]:::anat + A1[Albertson & Thomson 1976]:::anat end subgraph 1980-1990 A[White et al. 1986]:::anat & B[Durbin 1987]:::anat